A GUN military helicopter was flying over Station Square and Sonic was a prisoner onboard the craft.
"Attention, Control, we are currently heading south. Suspect is in custody." Pilot said on the radio.
"This is Control speaking. We've verified your position. Handle suspect carefully. He's a slippery little guy." Mission Control said over the radio.
Sonic was handcuffed and sitting between two GUN soldiers.
"You're awful quiet." a Soldier said.
"So what?" Sonic asked.
'They couldn't've found out! I have them with me!' she thought.
"Well, from what I heard, you've caused quite a ruckus over at Prison Island the other night. Now we can't get two words out of you."
"Guess I'm not feeling too chatty."
Another soldier stood up and menaced her with his gun.
"You better watch that smart mouth, hedgehog, or you'll be running laps in a ten-by-nine cell."
Suddenly Sonic created a ruckus on the chopper.
"What's going on up there?" Mission Control asked over the radio.
Then Sonic emerged from the helicopter and landed on the stabilizer wing.
"I gotta get the chump on these fly guys." she said.
"Hey! What do you think you're doin'? Come back!" the soldier said.
'Getting away from you.' Sonic thought, sawed off the stabilizer wing, rode it down toward the city, landed in a skating rink, rode it across a half-pipe, and ditched it.
"Sorry, dudes!" she said.
At GUN HQ.
"Suspect located!" Officer said.
"Deploy robots immediately!" another said.
"Roger!" another said.
In Central City Sonic reached the top of a hill on one of the roads, only to be met with a swarm of GUN Beetles that force him to run in opposite direction.
"I am outta here!" she said and dodged their laser damaging stoplights, cars, and even buildings. "Uh-oh. They mean business!" she said then thought about using her new powers but shook her head and ducked down a manhole while the Beetles flew past.
Soon she was walking through the sewer.
"Could I possibly sink any lower?" she asked. "What am I running away from, anyway? I mean, I haven't done anything wrong, have I? I just wonder what it is they think I did..." she said to herself. "I have them with me. They couldn't figure it out. I only teleported once to get here and Chaos Controlled not as Super Sonic to get to Station Square quicker and no one saw me."
Elsewhere Chris was walking in the sidewalk with another kid.
"Hey Chris, I heard you come from Station Square." a kid said.
"Uh... Yeah?" Chris said.
"Have you ever seen Sonic the Hedgehog up close?"
"Uh... Sonic? Well... sorta."
"What's she like? Is she really that fast?"
"You bet she's fast! She's faster than anybody, and she's nicer than anybody, too."
"Wish I could meet her. Heh, who knows, if we're lucky, maybe we'll both get to meet her someday."
"Well, I gotta get to class. Later!"
"See ya!"
As the kid left, Chris looked skyward.
In the President's limo Christina was reading a report.
"Mr. President, it appears our undercover operative has settled into his new mission and will have all of the resources necessary." Christina said.
"Good work. And what about the flood?" the president asked.
"Well, sir, I've read the full report over the last few days. There was some damage, but from what I can gather, none of the citizens were harmed in any way."
"And what about Sonic? Is there any new information?"
"I'm afraid it doesn't look good, and with a crime of this magnitude, sir, I'm not sure the government should get involved."
"I don't know. This just doesn't sound like her."
"I agree with you, sir. Sonic would never do such a thing. I think she's been wrongly accused, Mr. President, and I think you should do something about it." Sam said.
"Just drive."
"Either way, I don't feel it would look good for us to be involved. We should wash our hands of her." Christina said.
"Do you really think so?"
"I do, sir."
Suddenly Sam slam med in the brakes, throwing her into the glass.
"Are you crazy?! What are you trying to do?" she asked.
"I'm trying to do my job. Just driving." Sam said.
That night, the mysterious hedgehog showed up at the National Museum in front of an exhibit containing a Chaos Emerald. Immediately the alarms sound, and the hedgehog ran out, only to be met by several GUN Beetles. They fired at him, but he smirked and nimbly dodged them. Then he used a powerful energy destroying the Beetles as he made his getaway.
At the White House.
"Mr. President, I have some bad news. Sonic was just seen at the National Museum of Art attempting to steal the Chaos Emerald." commander said.
"It can't be." the president said.
"My men are awaiting your instructions, sir."
"We have no choice. Find her and place her under arrest."
Commander saluted.
"Yes, Mr. President. I'll alert all divisions immediately, sir." he said and left.
At GUN Headquarters.
"Attention all division commanders! Sonic the Hedgehog has gone underground. Let's go get her." Commander said.
Then a swarm of GUN Beetles took off into the night sky.
At the Thorndyke's apartment Chris, Chuck, Ella, Tanaka, Cream, and Cheese were watching the news.
"And now a breaking news story. I'm standing in the main pavilion in the Nation Museum of Art, where earlier tonight, a thief broke through security and stole a priceless Chaos Emerald. Authorities found these images on tapes confiscated from the museum's security cameras." News Reporter said.
The camera footage showed the mysterious hedgehog breaking the glass surrounding the Chaos Emerald. He appeared in front of the camera and grinned before making his getaway.
"Was that Sonic?" Chris asked.
"It can't be! Sonic would never take something that doesn't belong to her!" Cream said.
"Chao chao chao chao chao chao!" Cheese said.
"Yeah, right. That was Sonic on those security tapes." Chuck said.
The others became mad at him.
"It can't be!" Chris said.
"She was framed!" Ella and Tanaka said.
"That's right!" Cream said.
"Chao chao!" Cheese said.
"Uh... Maybe it wasn't her. I guess you can't always believe your eyes." Chuck said.
"Surprisingly enough, authorities have determined from this footage that the thief is none other than Sonic the Hedgehog. According to reports, Sonic has destroyed numerous government tanks and fled to an unknown location." New Reporter said.
"But there... there must be some kind of mistake. Sonic wouldn't..." Chris said and sighed.
"Of course she wouldn't, Mr. Chris. I'm sure there are some explanations." Ella said and Tanaka nodded.
Chris walked over to the window and looked up at the sky.
"Sonic... What's happening?" he said to himself.
At Central City the GUN Beetles blew up various sewer entrances and flew in.
In the sewer Jerome and several other poor men were huddled around a fire.
"What, are you crazy or somethin'? Sonic ain't no thief." a man said.
"I wouldn't make this up! I saw it on a TV in a repair shop window. Would I lie to you? No. I tell you, they saw her steal the thing." Jerome said.
"Hey!"
"And not only that, they caught her breaking into Prison Island just last night - red-handed. Probably trying to steal government secrets."
Then Sonic ran past them, with several GUN Beetles in pursuit.
In Prison Island Mr. Stewart drove Scarlet Garcia up to a security checkpoint.
"How did you manage to get permission for me to visit Prison Island?" Scarlet asked.
"Well, let's just say I have connections in high places." Mr. Stewart said and
Mr. Stewart showed his credentials to the camera then the doors in front of the car open, and the drove through.
"Who are you, exactly?"
"Just a fellow news hound, that's all."
Once inside, they interviewed the warden.
"Have you ever heard of a government operation called Project Shadow?" Scarlet asked.
"I'm afraid that's top-secret. However, after last night, I'm not sure how much longer it will stay secret. Take a look." Warden said and
The warden showed them security footage of Eggman giving the mysterious hedgehog the order to destroy a GUN robot.
"This is security cam video from last night. As you can see, Eggman and the hedgehog have broken into the system, and are trying to steal the Project Shadow file." he said and the footage ended.
"This video tape makes it clear as day. Sonic is no longer concerned with the safety of our citizens, and had decided to join forces with the enemy. She had us all fooled, didn't she?"
"What happens next, sir?" Mr. Stewart asked.
"Quite simple. We arrest her and try her for high treason."
A still of the mysterious black hedgehog was shown.
At Central City Sonic burst out of the sewer, then used the manhole cover to dive down and destroy the GUN Beetles.
After the Beetles were destroyed, Sonic put the manhole cover back.
"That was easy." she said then spotlight blinded her as a Big Foot landed nearby. "Can't hang around, big guy, sorry. I'll give you a ring some time, what do you say?" she said and held up a Power Ring, but the Big Foot started firing at hers and he easily dodged. "Now that's what I call a tight squeeze."
Then she activated the ring and home attacked the spotlight, destroying it.
The Big Foot reacted by firing eight missiles at Sonic. Sonic allowed to chase her up a building, then she landed on the Big Foot and jumped off, causing the missiles to destroy the robot.
"That guy's gotta work on his aim a little bit." she said.
Then a glow came from the destroyed robot.
Then the glow subsided, revealing the mysterious black hedgehog.
"What the...?"
"Good evening. I must say, it's a pleasure for me to finally meet you face-to-face, Sonic. We do look alike. It's uncanny." the hedgehog said.
"Wait a minute! So it's you who been getting me into all this hot water lately! Impostor!" she said and leapt toward the robot to attack the hedgehog, but he vanished before she got there.
At Prison Island Mr. Stewart was looking at the still of the hedgehog.
"It certainly looks like Sonic... but still, there's something strange, different about it." Mr. Stewart said to himself.
Back at Central City Sonic looked up to see the black hedgehog atop a building.
"I assure you, Sonic, I'm no impostor. I possess too much power to be anything but the real thing." the hedgehog said.
"Well, if you're so powerful, let's see you prove it!" Sonic said and ran up the building, but the hedgehog faded before she could get there.
She saw the other hedgehog atop a taller building and laughed.
"Hey, not bad. I'm almost impressed. How about a little race action?"
Soon she was racing the other hedgehog through the city. Notably, while she ran, the other hedgehog appeared to skate.
'This has to be who Andrew was talking about at the paper.' Sonic thought. 'Maybe I'll read it again later.'
At the apartment Chuck was on the phone.
"You're kidding! Unbelievable. Well, be sure to call us right away if anything else happens." he said and hung up. "That was your father. Apparently Sonic's been spotted battling a government robot on downhill street."
Chris instantly got up and ran out of the room.
"Chris, where are you going?" Ella asked.
"I will follow him, Mr. Thorndyke." Tanaka said and left.
"Slow down! I'll come with you." Chuck said and left to.
Back in Central City the hedgehog cut in front of Sonic.
"He's tougher than I remember hearing he was." Sonic said to herself. "Not quite." she said and caught up.
Tanaka was driving Chris and Chuck into the city when they saw Sonic and the other hedgehog running toward them. The black hedgehog vanished, and the car skid to a stop. The other hedgehog reappeared and kicked Sonic to the ground.
"What just happened?" she said and thought about what happened a few months ago.
Sonic was running trying to figure out where Station Square is when she was hit by something.
"Ooff!" she said and things started to go black.
When she opened her eyes she saw she was in some kind of lab.
"What?" she said seeing her hands and feet were trapped.
"So you can talk." she heard someone say.
"Who are you?" she asked.
"Dr. Andrew Grey." he said.
"What do you want?"
"An experiment that my friend did fifty years ago."
"Who?"
"Gerald Robotnik. He created something to look after his granddaughter Maria. Then GUN found out and it all went downhill from there. I want to make you the same thing."
"What are you going to do?"
"Give you everything you already have and what Gerald's experiment has but much, much, much stronger." he said.
"Which is?"
"You'll see. He has many things." he said then took out a needle and put it in her arm.
She felt it go in herself and felt a little dizzy.
Then she looked at him.
"What did you just do?" she asked. "I feel dizzy."
"You should be fine in a few minutes." he said. "And like I said, you'll see."
Ten minutes later Sonic felt fine.
"You feeling fine now?" Andrew asked.
"Yeah." Sonic said.
"Good. How strong do you feel compared to before I did this?"
"About five times as strong."
"Good. I have one thing to make then."
"Which is?"
"Something to help you control how much strength you use."
Sonic nodded.
"Anything unparticular? Gerald's has limiters on his wrists and ankles."
"I, I would be fine with a necklace."
"Alright then. I do have a heart. I'm only doing this for now."
Then he left and went to take care of the necklace.
"What is he doing with me?" Sonic said to herself.
An hour later Andrew was back with a necklace as a heart.
"I can tell your full of love so this is a heart." he said and put it on her getting her to feel less strength in her.
Then he let her go.
Before he could do anything Sonic kicked him hard, started running then saw paper with her name on it and saw it had everything she could now do so grabbed it and ran.
'He must've seen my bracelet and saw my name.' she thought while she ran.
When she was far away she stopped and opened the notes.
Like Gerald I've done it! It's not the same exactly but has everything he has. Everything is more than five times as strong as him. The necklace will be like his limiters to save power. Hopefully they'll meet someday and become close. Everything Project Shadow has now known as Project Sonic has.
While she read what he has and now she has she was shocked.
"I'm keeping this quiet. Hopefully no one will find this out." she said and ran.
Then a spy drone showed up.
At Eggman's base.
"Sonic's a bit overwhelmed, isn't she? I certainly can't blame her. I felt rather confused myself when I encountered Shadow for the first time." Eggman said.
In a flashback Prison Island after activating the Project Shadow machine, Eggman watched as the black hedgehog rose from his stasis chamber.
"What?! It's that hedgehog! How dare you deceive me, you speedy little slimeball!" he said and
The hedgehog climbed out of the chamber.
"Wait. You're not Sonic."
The hedgehog bowed.
"My name is Shadow. You've awakened me from a state of suspended animation, and I am very grateful. To show my gratitude, I am at your command." he said.
Then a GUN Hot Shot burst into the room.
"Bad timing as usual!" Eggman said.
"Wait. I will show you my power, Doctor." Shadow said and attacked and destroyed the robot.
Back in Eggman's base.
"You've met your match, Sonic! Compared to Shadow's fancy footwork, your as slow as a man of molasses! And now that you two have gotten a bit better acquainted, you're sure to see that for yourself!" Eggman said and laughed.
'But there's something about that medallion you wear now and that paper you were looking at that tells me something happened.' he thought seeing the heart necklace.
Back at Central City Shadow stood over a fallen Sonic, Chaos Emerald in hand. Then he held it up.
"He's got a Chaos Emerald!" Chris said.
"Where'd you get that Chaos Emerald, you phony freak? Hand it over!" Sonic said and Shadow teleported behind her.
"You can do better than that, Sonic. If you don't light a fire under those feet, you'll never get this Emerald back." Shadow said and she leapt into the air, and attempted to kick him, but he teleported again.
"He really is faster than I am!" she said shocked.
'Unless I let out my own new powers, speed and strength. But then they'll find out.' she thought.
"But that's not speed. He's disappearing!" Chuck said.
"Whoa!" Chris said.
Shadow was now on top of a street lamp.
"That's not all. I'm full of surprises." Shadow said.
"Grandpa!"
"Chaos Control now." Shadow said and activated Chaos Control while Sonic ran.
"He can cause Chaos Control with just one Chaos Emerald? Who is he? And there did he come from?" Sonic said to herself.
'I know I can Chaos Control without one but this is still ridiculous!'
Then Shadow reappeared next to her and delivered blow after blow.
"Leave her alone!" Chris said.
"Like to fight dirty, don'cha?" Sonic said.
"Consider yourself fortunate. If I'd used my full strength, you'd have been much worse off than this." Shadow said and overshadowed Sonic. "Many years ago, Professor Gerald Robotnik endowed me with the power of Chaos Control. A normal creature like yourself doesn't stand a chance against me."
'I'm not normal anymore.' she thought.
"Don't underestimate us "normal" types."
Shadow glanced up for a moment, hearing the sound of the approaching authorities, then looked back at her.
"I have a feeling I should make myself scarce. Goodbye, Sonic. It certainly was a nice pleasure. Chaos Control now." he said and used the Chaos Emerald to vanish as several police cars, helicopters, and GUN Beetles arrived.
"Sonic, we've got you surrounded! You're under arrest. Put your hands up!" a police officer said getting her to come back.
"No way! You can't arrest me! I didn't do anything! Honest!" she said.
Among the officers was Officer Albright.
"I'm gonna give you to the count of five to surrender! Ready? One... Two... Three... Four..." Albright said.
"Turn yourself in, Sonic! You're already in trouble. Just do as they say!" Chris said. "Please, Sonic..." he said with tears springing to his eyes.
"You're time's up, buddy! We've got a special cell on Prison Island with your name on it!"
"Did you just say Prison Island?" Sonic asked.
"Yeah, what about it?"
"Really, you mean that's where you're taking me from here?"
"That's where we usually take criminals."
"Okay, Chris, I'll do it. I'm gonna turn myself in." Sonic said and sat cross-legged. "All right, guys, cuff me. I'm all yours." she said to the officers.
"Get her!"
"Only just take it easy on the wrists, fellas." she said. "You might use Chaos Control like before, friend, but I'm gonna have to get out of this without tricks. I'll do it... somehow. I'm not exposing what I really can do, what and who I really am." she said to herself and was led in handcuffs to a helicopter. "Don't worry about me, Chris. I'll be out before you know it, buddy!"
"I hope so..." Chris said teary.
The helicopter took off and Shadow watched from a distance.
"I won't let anyone stand in my way. Least of all you, Sonic. Maria..." Shadow said to himself.
At Eggman's base Eggman and his hench-bots were celebrating their victory with Shadow.
"Yippee!" Eggman said.
"We did it! We did iiiit!" he said and shook Shadow's hand. "That hedgehog's in the hoosegow thanks to you, Shadow!"
"He is practically busting his buttons." Decoe said.
"That jacket always was tight around the tummy." Bocoe said.
"Remember, Doctor, you must still obtain five more Chaos Emeralds in order to use the Eclipse Cannon. But when you do, it will give you ultimate power and make you master of the universe." Shadow said.
"Sounds good to me! And now to has out the rest of our dastardly strategy. Let's see..." Eggman said.
Then Bokkun flew in holding his TV.
"Doctor, I have a message for you this time!" he said and giggled then tossed the screen to Eggman, and it activated.
Rouge was holding a bouquet of roses.
"Hiya, Doc. Long time no see. I was wondering if we could get together to discuss a little business transaction?" Rouge said.
"A business transaction?" Decoe said.
"I would not trust her, Doctor." Bocoe said.
"Who asked you, bolt-brain?! Fetch her right away!" Eggman said.
"Uh-oh!" Decoe said.
"Here we go!" Bocoe said.
The outside of the pyramid base was shown while the TV explodes. Bokkun laughed.
"That's not funny!" Eggman said.
"Don't blame me! Lots of stuff have television bombs!" Bokkun said.
Rouge dropped in still holding her roses.
"I just hope this little scam of mine works." she said.
"Oh! I didn't expect you so soon." Eggman said.
"Good evening, Doctor. I've got a little something I'd like to show you." she said and showed him the blue Chaos Emerald she acquired at Angel Island.
"A Chaos Emerald..."
"It's all yours, Eggy, if you agree to my conditions. All you have to do is be a good boy and play nice, and I'll tell you where the others are. What do you say, Doc? Do we have a deal?"
Shadow scoffed.
"That depends. What do you want?"
Shadow started to see a vision of Maria.
"Pleasure before business. Who's this charming friend of yours? I'm Rouge the Bat. What's your name?"
"It's Shadow." Shadow said and turned to her face. "Shadow the Hedgehog."
Rouge was startled by Shadow's ruby red eyes.
At the harbor Chuck, Ella, Cream, and Cheese watched as Tanaka and Chris boarded a ship dressed in black outfits and hats.
"Don't worry, you guys. We'll be back soon. But... this is something I have to find out for myself." Chris said.
"We understand, Chris. You two take care of yourselves." Chuck said.
"Why do we have to dress like this, Mr. Tanaka?
"I've been inspired by my boyhood hero." Tanaka said.
Meanwhile Tails and Amy were on the X-Tornado also on the move. Amy was impatient.
"Come on! Step on it! We've got to get to Prison Island in a hurry!" Amy said.
"What a bossy-" Tails started.
"What did you say?"
"Uh..."
At Prison Island Sonic was sitting alone in her chamber. It was surrounded on all sides by water, making it practically escape-proof. There were various mathematical formulas on the walls.
"What a day... Who'd have thought I'd be thrown in jail for something I didn't do? I'd better think fast, use my time wisely, and figure out who that Shadow was now, and what he wants." she said to herself.
'Since I can't take this paper out I'll have to wait a while.' she thought and played with her necklace. 'I'm not risking them to know what I really am now. At least I know what he said when he was making me was true and where he came up with the idea of making me and what abilities I have now.'